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RitchieLabIGH / IRFinder

MIT License
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IRFinder Diff Arguments #9

Closed jscaber closed 2 years ago

jscaber commented 2 years ago

Hi Claudio,

hopefully last issue: I haven't found an easy way of passing arguments to IRFinder diff. Is there an easy way to pass lists of files to the arguments other than moving/softlinking into subfolders by experimental group?

My command (which does not work as the argparser does not recognise commas):

singularity run -H $PWD:/home     /MYPATH/IRFinder Diff    \
-g:CTR IRFinder.dir/File1_1/IRFinder-IR-dir.txt,IRFinder.dir/File1_2/IRFinder-IR-dir.txt,IRFinder.dir/File1_3/IRFinder-IR-dir.txt,IRFinder.dir/File2_1/IRFinder-IR-dir.txt,IRFinder.dir/File2_2/IRFinder-IR-dir.txt,IRFinder.dir/File2_3/IRFinder-IR-dir.txt     \
-g:DIS IRFinder.dir/File3_1/IRFinder-IR-nondir.txt,IRFinder.dir/File3_2/IRFinder-IR-nondir.txt,IRFinder.dir/File3_3/IRFinder-IR-nondir.txt,IRFinder.dir/File4_1/IRFinder-IR-nondir.txt,IRFinder.dir/File4_2/IRFinder-IR-nondir.txt,IRFinder.dir/File4_3/IRFinder-IR-nondir.txt     \
-ir 0.05     -o results.dir/IRFinder/EXP         \
> results.dir/IRFinder/EXP/EXP.design.tsv.log

Many thanks if you have any suggestions other than softlinking into subfolders with * commands as in the example given in the help section.

Best wishes, Jakub

jscaber commented 2 years ago

Managed to work it out: each needs the same -g:CONDITION which can be repeated as many times as needed. J

singularity run -H $PWD:/home     /MYPATH/IRFinder Diff    \
-g:CTR IRFinder.dir/File1_1/IRFinder-IR-dir.txt \
-g:CTR IRFinder.dir/File1_2/IRFinder-IR-dir.txt\
etc.....\
-g:DIS IRFinder.dir/File3_1/IRFinder-IR-dir.txt
-g:DIS IRFinder.dir/File3_2/IRFinder-IR-dir.txt
etc......\
-ir 0.05     -o results.dir/IRFinder/EXP         \
> results.dir/IRFinder/EXP/EXP.design.tsv.log
CloXD commented 2 years ago

Hello Jackub, sorry for the late answer. An easier way is to give the files as a space-separated list ( that is the way bash return a list of matches). In your case:

singularity run -H $PWD:/home     /MYPATH/IRFinder Diff    \
-g:CTR IRFinder.dir/File1_1/IRFinder-IR-dir.txt IRFinder.dir/File1_2/IRFinder-IR-dir.txt IRFinder.dir/File1_3/IRFinder-IR-dir.txt IRFinder.dir/File2_1/IRFinder-IR-dir.txt IRFinder.dir/File2_2/IRFinder-IR-dir.txt IRFinder.dir/File2_3/IRFinder-IR-dir.txt     \
-g:DIS IRFinder.dir/File3_1/IRFinder-IR-nondir.txt IRFinder.dir/File3_2/IRFinder-IR-nondir.txt IRFinder.dir/File3_3/IRFinder-IR-nondir.txt IRFinder.dir/File4_1/IRFinder-IR-nondir.txt IRFinder.dir/File4_2/IRFinder-IR-nondir.txt IRFinder.dir/File4_3/IRFinder-IR-nondir.txt     \
-ir 0.05     -o results.dir/IRFinder/EXP         \
> results.dir/IRFinder/EXP/EXP.design.tsv.log

Cheers, Claudio